Generated diagrams do not correspond to propect structure

What I've encountered:

Some packages were skipped
Consecutively generated diagrams on same directory do not match
For some set of packages, all diagrams were identical to the one generated for first package of that set.

Project structure (After diagrams created): (For reference, generated diagrams are attached as images)

app
- root
  - model
  - ownerships
    - estate
      - Estate.java
    - vehicle
      - Type.java
      - Vehicle.java
    - Ownership.java
    - ownerships.plantuml # contains only Ownership.java interface
  - InvoiceImpl.java
  - Invoice.java
  - User.java
- repository/:
  - control/:
    - control.plantuml # correctly represents relationship between classes in repository (not control) package
    - PaymentTriggerImpl.java
    - PaymentTrigger.java
  - repository.plantuml # is exactly same as ownerships.plantuml
  - Users.java
- service.taxcounter/:
  - resolvers/: # no diagrams here...
    - TaxResolver.java
  - TaxCounterImpl.java
  - TaxCounter.java
  - TaxResolvers.java
- webapi/:
  - ErrorController.java
  - ServletConfig.java
- RootConfig.java
WebAppInit.java

Also, at the root of Intellij project the correct diagram was created. But it is really messy with package names: I think that the outermost package's name should be the only absolute path. All inner packages should be relative to their respective parent packages.

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